5gyr: Difference between revisions
New page: '''Unreleased structure''' The entry 5gyr is ON HOLD Authors: Masaru Yamanaka, Makoto Hoshizumi, Satoshi Nagao, Ryoko Nakayama, Naoki Shibata, Yoshiki Higuchi, Shun Hirota Description:... |
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The | ==Tetrameric Allochromatium vinosum cytochrome c'== | ||
<StructureSection load='5gyr' size='340' side='right'caption='[[5gyr]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5gyr]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Allochromatium_vinosum_DSM_180 Allochromatium vinosum DSM 180]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GYR FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5gyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gyr OCA], [https://pdbe.org/5gyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gyr RCSB], [https://www.ebi.ac.uk/pdbsum/5gyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gyr ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CYCP_ALLVD CYCP_ALLVD] Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The number of artificial protein supramolecules has been increasing; however, control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homodimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers. The X-ray crystal structure of oxidized tetrameric AVCP consisted of two monomer subunits and one domain-swapped dimer subunit, which exchanged the region containing helices alphaA and alphaB between protomers. The active site structures of the domain-swapped dimer subunit and monomer subunits in the tetramer were similar to those of the monomer subunits in the native dimer. The subunit-subunit interactions at the interfaces of the domain-swapped dimer and monomer subunits in the tetramer were also similar to the subunit-subunit interaction in the native dimer. Reduced tetrameric AVCP dissociated to a domain-swapped dimer and two monomers upon CO binding. Without monomers, the domain-swapped dimers formed tetramers, hexamers, and higher-order oligomers in the absence of CO, whereas the oligomers dissociated to domain-swapped dimers in the presence of CO, demonstrating that the domain-swapped dimer maintains the CO-induced subunit dissociation behavior of native ACVP. These results suggest that protein oligomer formation may be controlled by utilizing domain swapping for a dimer-monomer transition protein. | |||
Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers.,Yamanaka M, Hoshizumi M, Nagao S, Nakayama R, Shibata N, Higuchi Y, Hirota S Protein Sci. 2017 Mar;26(3):464-474. doi: 10.1002/pro.3090. Epub 2017 Feb 14. PMID:27883268<ref>PMID:27883268</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5gyr" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Allochromatium vinosum DSM 180]] | |||
[[Category: Large Structures]] | |||
[[Category: Higuchi Y]] | |||
[[Category: Hirota S]] | |||
[[Category: Hoshizumi M]] | |||
[[Category: Nagao S]] | |||
[[Category: Nakayama R]] | |||
[[Category: Shibata N]] | |||
[[Category: Yamanaka M]] | |||
Latest revision as of 14:46, 2 August 2023
Tetrameric Allochromatium vinosum cytochrome c'Tetrameric Allochromatium vinosum cytochrome c'
Structural highlights
FunctionCYCP_ALLVD Cytochrome c' is the most widely occurring bacterial c-type cytochrome. Cytochromes c' are high-spin proteins and the heme has no sixth ligand. Their exact function is not known. Publication Abstract from PubMedThe number of artificial protein supramolecules has been increasing; however, control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homodimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers. The X-ray crystal structure of oxidized tetrameric AVCP consisted of two monomer subunits and one domain-swapped dimer subunit, which exchanged the region containing helices alphaA and alphaB between protomers. The active site structures of the domain-swapped dimer subunit and monomer subunits in the tetramer were similar to those of the monomer subunits in the native dimer. The subunit-subunit interactions at the interfaces of the domain-swapped dimer and monomer subunits in the tetramer were also similar to the subunit-subunit interaction in the native dimer. Reduced tetrameric AVCP dissociated to a domain-swapped dimer and two monomers upon CO binding. Without monomers, the domain-swapped dimers formed tetramers, hexamers, and higher-order oligomers in the absence of CO, whereas the oligomers dissociated to domain-swapped dimers in the presence of CO, demonstrating that the domain-swapped dimer maintains the CO-induced subunit dissociation behavior of native ACVP. These results suggest that protein oligomer formation may be controlled by utilizing domain swapping for a dimer-monomer transition protein. Formation and carbon monoxide-dependent dissociation of Allochromatium vinosum cytochrome c' oligomers using domain-swapped dimers.,Yamanaka M, Hoshizumi M, Nagao S, Nakayama R, Shibata N, Higuchi Y, Hirota S Protein Sci. 2017 Mar;26(3):464-474. doi: 10.1002/pro.3090. Epub 2017 Feb 14. PMID:27883268[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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